Prepare the glasses: Remove a strip of zest from one of the limes using a vegetable peeler. Juice the limes; you’ll need 6 tablespoons (3 ounces) juice. Spread 3 tablespoons salt on a small plate. Rub the lime peel and a little of the juice around the rims of 6 glasses and then dip the rims in the salt. Fill the glasses with ice.
Make the margaritas: In a pitcher, stir together the tequila, Cointreau, chile slices, red pepper flakes and lime juice. Pour into the glasses.